It's because IPS is more than ten years old, and UPS less than one. Human nature is such that we prefer what we're used to, regardless of technical merit.many people still seem to prefer IPS files rather than UPS (IMHO), are there any advantages in using UPS instead of IPS?.
The advantages are being able unpatch a hard-patched game with the same file, support for files larger than 16MB (required for GBA/NDS), more optimized and simplified file format that leaves compression up to true archivers (smaller patches), and you can actually verify if you patched correctly or not.
The last one is the biggest allure. While Genesis is nowhere near as bad as the SNES in this regard, let's say someone makes a patch against an interleaved SMD file. But your ROM is BIN. Your patch won't work, because it has no way of knowing whether the patch was made against the SMD or BIN version. With UPS, a quick CRC check will tell you.
It can also warn you if you patched the wrong version of a ROM, too. So you don't get random errors while playing.